Well, here's my experience with ShopSite page creation and menus. We don't use ShopSite page links feature to create our navigation. I use a ShopSite Include (in the custom templates area) to have a single "Navigation" include with the HTML for our navigation. It's super easy to change if we add/remove pages, and it we can include it everywhere, even on product more-info pages and the cart.
Then, for more flexibility, you can use ShopSite page links feature to add depth to your categories. Have a standard navigation bar, such as a sidebar or top horizontal navbar and then break down into subcategories using the ShopSite page links feature. Then you can have sub-pages and you can link to main categories from your navbar include.
For an example, check out
http://www.formalsexpress.com and click on the "Prom Dresses" category. The top navigation bar is just an include, so we can use the "Page Links" to create the links to sub-category pages from individual pages.
Make any sense?